I'm a masters student attempting to conduct a parentage analysis on a population of fish for my thesis. My advisor and post-docs haven't been very helpful, so I need some help! I have dinucleotide microsatellite markers that I've run on a set of individuals.
I'm using GeneMapper 4.0 to score the alleles of said markers but something isn't making sense. My alleles are shifted to where they are not evenly distributed in their sizes. For example, at a given locus for one individual I have one allele peak at 152 while the other allele peak is at 161 (It's an obvious heterozygote).
This "shift" doesn't make sense considering my markers are dinucleotide and should be spaced 2 bp apart, right? So either 152 is actually 151/153 or 161 is actually 162/160. How can I score these and resolve this issue while keeping consistency for my analysis later? I see this shift everywhere and I've already ruled out contamination and I'm positive these peaks are real. Any pop gen people out there that have a clue what to do?
I've been stuck on this for weeks, no amount of web searching/paper reading helped. Thanks!